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<title>kspace_style command — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<div class="section" id="kspace-style-command">
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<span id="index-0"></span><h1>kspace_style command<a class="headerlink" href="#kspace-style-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>kspace_style style value
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</pre></div>
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</div>
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<ul class="simple">
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<li>style = <em>none</em> or <em>ewald</em> or <em>ewald/disp</em> or <em>ewald/omp</em> or <em>pppm</em> or <em>pppm/cg</em> or <em>pppm/disp</em> or <em>pppm/tip4p</em> or <em>pppm/stagger</em> or <em>pppm/disp/tip4p</em> or <em>pppm/gpu</em> or <em>pppm/omp</em> or <em>pppm/cg/omp</em> or <em>pppm/tip4p/omp</em> or <em>msm</em> or <em>msm/cg</em> or <em>msm/omp</em> or <em>msm/cg/omp</em></li>
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</ul>
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<pre class="literal-block">
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<em>none</em> value = none
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<em>ewald</em> value = accuracy
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accuracy = desired relative error in forces
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<em>ewald/disp</em> value = accuracy
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accuracy = desired relative error in forces
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<em>ewald/omp</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm/cg</em> value = accuracy (smallq)
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accuracy = desired relative error in forces
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smallq = cutoff for charges to be considered (optional) (charge units)
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<em>pppm/disp</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm/tip4p</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm/disp/tip4p</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm/gpu</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm/omp</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm/cg/omp</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm/tip4p/omp</em> value = accuracy
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accuracy = desired relative error in forces
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<em>pppm/stagger</em> value = accuracy
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accuracy = desired relative error in forces
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<em>msm</em> value = accuracy
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accuracy = desired relative error in forces
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<em>msm/cg</em> value = accuracy (smallq)
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accuracy = desired relative error in forces
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smallq = cutoff for charges to be considered (optional) (charge units)
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<em>msm/omp</em> value = accuracy
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accuracy = desired relative error in forces
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<em>msm/cg/omp</em> value = accuracy (smallq)
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accuracy = desired relative error in forces
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smallq = cutoff for charges to be considered (optional) (charge units)
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>kspace_style pppm 1.0e-4
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kspace_style pppm/cg 1.0e-5 1.0e-6
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kspace style msm 1.0e-4
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kspace_style none
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Define a long-range solver for LAMMPS to use each timestep to compute
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long-range Coulombic interactions or long-range 1/r^6 interactions.
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Most of the long-range solvers perform their computation in K-space,
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hence the name of this command.</p>
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<p>When such a solver is used in conjunction with an appropriate pair
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style, the cutoff for Coulombic or 1/r^N interactions is effectively
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infinite. If the Coulombic case, this means each charge in the system
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interacts with charges in an infinite array of periodic images of the
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simulation domain.</p>
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<p>Note that using a long-range solver requires use of a matching <code class="xref doc docutils literal"><span class="pre">pair</span> <span class="pre">style</span></code> to perform consistent short-range pairwise
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calculations. This means that the name of the pair style contains a
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matching keyword to the name of the KSpace style, as in this table:</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="49%" />
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<col width="51%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>Pair style</td>
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<td>KSpace style</td>
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</tr>
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<tr class="row-even"><td>coul/long</td>
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<td>ewald or pppm</td>
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</tr>
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<tr class="row-odd"><td>coul/msm</td>
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<td>msm</td>
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</tr>
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<tr class="row-even"><td>lj/long or buck/long</td>
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<td>disp (for dispersion)</td>
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</tr>
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<tr class="row-odd"><td>tip4p/long</td>
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<td>tip4p</td>
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</tr>
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</tbody>
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</table>
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<hr class="docutils" />
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<p>The <em>ewald</em> style performs a standard Ewald summation as described in
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any solid-state physics text.</p>
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<p>The <em>ewald/disp</em> style adds a long-range dispersion sum option for
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1/r^6 potentials and is useful for simulation of interfaces
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<a class="reference internal" href="pair_lj_long.html#veld"><span>(Veld)</span></a>. It also performs standard Coulombic Ewald summations,
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but in a more efficient manner than the <em>ewald</em> style. The 1/r^6
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capability means that Lennard-Jones or Buckingham potentials can be
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used without a cutoff, i.e. they become full long-range potentials.
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The <em>ewald/disp</em> style can also be used with point-dipoles
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<a class="reference internal" href="pair_dipole.html#toukmaji"><span>(Toukmaji)</span></a> and is currently the only kspace solver in
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LAMMPS with this capability.</p>
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<hr class="docutils" />
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<p>The <em>pppm</em> style invokes a particle-particle particle-mesh solver
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<a class="reference internal" href="#hockney"><span>(Hockney)</span></a> which maps atom charge to a 3d mesh, uses 3d FFTs
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to solve Poisson’s equation on the mesh, then interpolates electric
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fields on the mesh points back to the atoms. It is closely related to
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the particle-mesh Ewald technique (PME) <a class="reference internal" href="#darden"><span>(Darden)</span></a> used in
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AMBER and CHARMM. The cost of traditional Ewald summation scales as
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N^(3/2) where N is the number of atoms in the system. The PPPM solver
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scales as Nlog(N) due to the FFTs, so it is almost always a faster
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choice <a class="reference internal" href="#pollock"><span>(Pollock)</span></a>.</p>
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<p>The <em>pppm/cg</em> style is identical to the <em>pppm</em> style except that it
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has an optimization for systems where most particles are uncharged.
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Similarly the <em>msm/cg</em> style implements the same optimization for <em>msm</em>.
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The optional <em>smallq</em> argument defines the cutoff for the absolute
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charge value which determines whether a particle is considered charged
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or not. Its default value is 1.0e-5.</p>
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<p>The <em>pppm/tip4p</em> style is identical to the <em>pppm</em> style except that it
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adds a charge at the massless 4th site in each TIP4P water molecule.
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It should be used with <a class="reference internal" href="pair_style.html"><em>pair styles</em></a> with a
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<em>tip4p/long</em> in their style name.</p>
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<p>The <em>pppm/stagger</em> style performs calculations using two different
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meshes, one shifted slightly with respect to the other. This can
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reduce force aliasing errors and increase the accuracy of the method
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for a given mesh size. Or a coarser mesh can be used for the same
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target accuracy, which saves CPU time. However, there is a trade-off
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since FFTs on two meshes are now performed which increases the
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compuation required. See <a class="reference internal" href="#cerutti"><span>(Cerutti)</span></a>, <a class="reference internal" href="#neelov"><span>(Neelov)</span></a>,
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and <a class="reference internal" href="#hockney"><span>(Hockney)</span></a> for details of the method.</p>
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<p>For high relative accuracy, using staggered PPPM allows the mesh size
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to be reduced by a factor of 2 in each dimension as compared to
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regular PPPM (for the same target accuracy). This can give up to a 4x
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speedup in the KSpace time (8x less mesh points, 2x more expensive).
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However, for low relative accuracy, the staggered PPPM mesh size may
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be essentially the same as for regular PPPM, which means the method
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will be up to 2x slower in the KSpace time (simply 2x more expensive).
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For more details and timings, see
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<a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Using <em>pppm/stagger</em> may not give the same increase in
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the accuracy of energy and pressure as it does in forces, so some
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caution must be used if energy and/or pressure are quantities of
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interest, such as when using a barostat.</p>
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</div>
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<hr class="docutils" />
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<p>The <em>pppm/disp</em> and <em>pppm/disp/tip4p</em> styles add a mesh-based long-range
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dispersion sum option for 1/r^6 potentials <a class="reference internal" href="#isele-holder"><span>(Isele-Holder)</span></a>,
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similar to the <em>ewald/disp</em> style. The 1/r^6 capability means
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that Lennard-Jones or Buckingham potentials can be used without a cutoff,
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i.e. they become full long-range potentials.</p>
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<p>For these styles, you will possibly want to adjust the default choice of
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parameters by using the <a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a> command.
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This can be done by either choosing the Ewald and grid parameters, or
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by specifying separate accuracies for the real and kspace
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calculations. When not making any settings, the simulation will stop with
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an error message. Further information on the influence of the parameters
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and how to choose them is described in <a class="reference internal" href="#isele-holder"><span>(Isele-Holder)</span></a>,
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<a class="reference internal" href="#isele-holder2"><span>(Isele-Holder2)</span></a> and the
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<a class="reference internal" href="Section_howto.html#howto-24"><span>How-To</span></a> discussion.</p>
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<hr class="docutils" />
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">All of the PPPM styles can be used with
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single-precision FFTs by using the compiler switch -DFFT_SINGLE for
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the FFT_INC setting in your lo-level Makefile. This setting also
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changes some of the PPPM operations (e.g. mapping charge to mesh and
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interpolating electric fields to particles) to be performed in single
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precision. This option can speed-up long-range calulations,
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particularly in parallel or on GPUs. The use of the -DFFT_SINGLE flag
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is discussed in <a class="reference internal" href="Section_start.html#start-2-4"><span>this section</span></a> of the
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manual. MSM does not currently support the -DFFT_SINGLE compiler switch.</p>
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</div>
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<hr class="docutils" />
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<p>The <em>msm</em> style invokes a multi-level summation method MSM solver,
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<a class="reference internal" href="#hardy"><span>(Hardy)</span></a> or <a class="reference internal" href="#hardy2"><span>(Hardy2)</span></a>, which maps atom charge to a 3d
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mesh, and uses a multi-level hierarchy of coarser and coarser meshes
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on which direct coulomb solves are done. This method does not use
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FFTs and scales as N. It may therefore be faster than the other
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K-space solvers for relatively large problems when running on large
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core counts. MSM can also be used for non-periodic boundary conditions and
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for mixed periodic and non-periodic boundaries.</p>
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<p>MSM is most competitive versus Ewald and PPPM when only relatively
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low accuracy forces, about 1e-4 relative error or less accurate,
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are needed. Note that use of a larger coulomb cutoff (i.e. 15
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angstroms instead of 10 angstroms) provides better MSM accuracy for
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both the real space and grid computed forces.</p>
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<p>Currently calculation of the full pressure tensor in MSM is expensive.
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Using the <a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a> <em>pressure/scalar yes</em>
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command provides a less expensive way to compute the scalar pressure
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(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
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to run an isotropic barostat. If the full pressure tensor is needed,
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then calculating the pressure at every timestep or using a fixed
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pressure simulation with MSM will cause the code to run slower.</p>
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<hr class="docutils" />
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<p>The specified <em>accuracy</em> determines the relative RMS error in per-atom
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forces calculated by the long-range solver. It is set as a
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dimensionless number, relative to the force that two unit point
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charges (e.g. 2 monovalent ions) exert on each other at a distance of
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1 Angstrom. This reference value was chosen as representative of the
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magnitude of electrostatic forces in atomic systems. Thus an accuracy
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value of 1.0e-4 means that the RMS error will be a factor of 10000
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smaller than the reference force.</p>
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<p>The accuracy setting is used in conjunction with the pairwise cutoff
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to determine the number of K-space vectors for style <em>ewald</em> or the
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grid size for style <em>pppm</em> or <em>msm</em>.</p>
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<p>Note that style <em>pppm</em> only computes the grid size at the beginning of
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a simulation, so if the length or triclinic tilt of the simulation
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cell increases dramatically during the course of the simulation, the
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accuracy of the simulation may degrade. Likewise, if the
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<a class="reference internal" href="kspace_modify.html"><em>kspace_modify slab</em></a> option is used with
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shrink-wrap boundaries in the z-dimension, and the box size changes
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dramatically in z. For example, for a triclinic system with all three
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tilt factors set to the maximum limit, the PPPM grid should be
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increased roughly by a factor of 1.5 in the y direction and 2.0 in the
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z direction as compared to the same system using a cubic orthogonal
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simulation cell. One way to ensure the accuracy requirement is being
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met is to run a short simulation at the maximum expected tilt or
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length, note the required grid size, and then use the
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<a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a> <em>mesh</em> command to manually set the
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PPPM grid size to this value.</p>
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<p>RMS force errors in real space for <em>ewald</em> and <em>pppm</em> are estimated
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using equation 18 of <a class="reference internal" href="#kolafa"><span>(Kolafa)</span></a>, which is also referenced as
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equation 9 of <a class="reference internal" href="#petersen"><span>(Petersen)</span></a>. RMS force errors in K-space for
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<em>ewald</em> are estimated using equation 11 of <a class="reference internal" href="#petersen"><span>(Petersen)</span></a>,
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which is similar to equation 32 of <a class="reference internal" href="#kolafa"><span>(Kolafa)</span></a>. RMS force
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errors in K-space for <em>pppm</em> are estimated using equation 38 of
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<a class="reference internal" href="#deserno"><span>(Deserno)</span></a>. RMS force errors for <em>msm</em> are estimated
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using ideas from chapter 3 of <a class="reference internal" href="#hardy"><span>(Hardy)</span></a>, with equation 3.197
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of particular note. When using <em>msm</em> with non-periodic boundary
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conditions, it is expected that the error estimation will be too
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pessimistic. RMS force errors for dipoles when using <em>ewald/disp</em>
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are estimated using equations 33 and 46 of <a class="reference internal" href="pair_polymorphic.html#wang"><span>(Wang)</span></a>.</p>
|
|
<p>See the <a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a> command for additional
|
|
options of the K-space solvers that can be set, including a <em>force</em>
|
|
option for setting an absoulte RMS error in forces, as opposed to a
|
|
relative RMS error.</p>
|
|
<hr class="docutils" />
|
|
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
|
functionally the same as the corresponding style without the suffix.
|
|
They have been optimized to run faster, depending on your available
|
|
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
|
|
of the manual. The accelerated styles take the same arguments and
|
|
should produce the same results, except for round-off and precision
|
|
issues.</p>
|
|
<p>More specifically, the <em>pppm/gpu</em> style performs charge assignment and
|
|
force interpolation calculations on the GPU. These processes are
|
|
performed either in single or double precision, depending on whether
|
|
the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
|
|
discussed above. The FFTs themselves are still calculated on the CPU.
|
|
If <em>pppm/gpu</em> is used with a GPU-enabled pair style, part of the PPPM
|
|
calculation can be performed concurrently on the GPU while other
|
|
calculations for non-bonded and bonded force calculation are performed
|
|
on the CPU.</p>
|
|
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
|
KOKKOS, USER-OMP, and OPT packages respectively. They are only
|
|
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
|
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
|
|
more instructions on how to use the accelerated styles effectively.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>Note that the long-range electrostatic solvers in LAMMPS assume conducting
|
|
metal (tinfoil) boundary conditions for both charge and dipole
|
|
interactions. Vacuum boundary conditions are not currently supported.</p>
|
|
<p>The <em>ewald/disp</em>, <em>ewald</em>, <em>pppm</em>, and <em>msm</em> styles support
|
|
non-orthogonal (triclinic symmetry) simulation boxes. However, triclinic
|
|
simulation cells may not yet be supported by suffix versions of these
|
|
styles (such as <em>pppm/cuda</em>).</p>
|
|
<p>All of the kspace styles are part of the KSPACE package. They are
|
|
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info. Note that
|
|
the KSPACE package is installed by default.</p>
|
|
<p>For MSM, a simulation must be 3d and one can use any combination of
|
|
periodic, non-periodic, or shrink-wrapped boundaries (specified using
|
|
the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command).</p>
|
|
<p>For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions.
|
|
The only exception is if the slab option is set with <a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a>,
|
|
in which case the xy dimensions must be periodic and the z dimension must be
|
|
non-periodic.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a>, <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/long</em></a>, <a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/long</em></a>, <a class="reference internal" href="pair_lj_long.html"><em>pair_style lj/long/coul/long</em></a>, <a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/long</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>kspace_style none
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p id="darden"><strong>(Darden)</strong> Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).</p>
|
|
<p id="deserno"><strong>(Deserno)</strong> Deserno and Holm, J Chem Phys, 109, 7694 (1998).</p>
|
|
<p id="hockney"><strong>(Hockney)</strong> Hockney and Eastwood, Computer Simulation Using Particles,
|
|
Adam Hilger, NY (1989).</p>
|
|
<p id="kolafa"><strong>(Kolafa)</strong> Kolafa and Perram, Molecular Simualtion, 9, 351 (1992).</p>
|
|
<p id="petersen"><strong>(Petersen)</strong> Petersen, J Chem Phys, 103, 3668 (1995).</p>
|
|
<p id="wang"><strong>(Wang)</strong> Wang and Holm, J Chem Phys, 115, 6277 (2001).</p>
|
|
<p id="pollock"><strong>(Pollock)</strong> Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).</p>
|
|
<p id="cerutti"><strong>(Cerutti)</strong> Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
|
|
and Computation 5, 2322 (2009)</p>
|
|
<p id="neelov"><strong>(Neelov)</strong> Neelov, Holm, J Chem Phys 132, 234103 (2010)</p>
|
|
<p id="veld"><strong>(Veld)</strong> In ‘t Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).</p>
|
|
<p id="toukmaji"><strong>(Toukmaji)</strong> Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
|
|
10913 (2000).</p>
|
|
<p id="isele-holder"><strong>(Isele-Holder)</strong> Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).</p>
|
|
<p id="isele-holder2"><strong>(Isele-Holder2)</strong> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory
|
|
Comput 9, 5412 (2013).</p>
|
|
<p id="hardy"><strong>(Hardy)</strong> David Hardy thesis: Multilevel Summation for the Fast
|
|
Evaluation of Forces for the Simulation of Biomolecules, University of
|
|
Illinois at Urbana-Champaign, (2006).</p>
|
|
<p id="hardy2"><strong>(Hardy)</strong> Hardy, Stone, Schulten, Parallel Computing 35 (2009)
|
|
164-177.</p>
|
|
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